akoya file format

[Watkins, Simon C-2]

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Colleagues, has anyone developed or have a solution for porting data sets from the Akoya platform (specifically the Vectra in our case) to an OME TIFF?
We have been given the option or rescanning a ton of slides on one of our systems or finding a way to convert previously scanned data
Thanks for the wisdom and of course stay safe!
S

Simon C. Watkins Ph.D
Distinguished Professor and Vice Chair Cell Biology
Professor Immunology
Director Center for Biologic Imaging
University of Pittsburgh
Bsts 225 3550 terrace st
Pittsburgh PA 15261
[hidden email]<mailto:[hidden email]>
Www.cbi.pitt.edu<http://www.cbi.pitt.edu/>
phone:[phone]

[Zalavadia, Ajaykumar]

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Simon,

Bio-Formats Command Line Tools supports converting qptiff to ome.tiff, bio-fromats seems to carryover metadata (channel names and spatial resolution) nicely.

A simple command like this should work:
bfconvert input.qptiff output.ome.tiff

There other flags you can pass while converting depending on your requirements, such as:
-noflat -bigtiff -tilex 512 -tiley 512 -compression LZW -pyramid-resolutions 4 -pyramid-scale 2

If the channels in your qptiff have cross talks and plenty of auto fluorescence then it might be better to unmix them in to component data using inForm first. You can merge component images using something like QuPath. On a side note: QuPath works very well with qptiff files, it uses bio-formats to read qptiff files. It should also be possible to write a script in QuPath to batch convert files.

I have found Image.sc<https://forum.image.sc/search?q=bfconvert> forums to be very resourceful for discussions related to ome.tiff  conversion and QuPath<https://qupath.github.io/>.

Best,
Ajay Zalavadia, Ph.D.
Imaging Specialist, Imaging Core  |  Lerner Research Institute
9500 Euclid Avenue NB10  |  Cleveland, OH 44195
Phone: [phone] | email: [hidden email]<mailto:[hidden email]>


From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Watkins, Simon C
Sent: Friday, January 22, 2021 7:57 AM
To: [hidden email]
Subject: [EXT] akoya file format

CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and that you believe it to be safe. If you feel this email cannot be trusted, please delete the message; or submit for investigation with the Report Phishing button or by forwarding the email to [hidden email]<mailto:[hidden email]>.

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*****

Colleagues, has anyone developed or have a solution for porting data sets from the Akoya platform (specifically the Vectra in our case) to an OME TIFF?
We have been given the option or rescanning a ton of slides on one of our systems or finding a way to convert previously scanned data
Thanks for the wisdom and of course stay safe!
S

Simon C. Watkins Ph.D
Distinguished Professor and Vice Chair Cell Biology
Professor Immunology
Director Center for Biologic Imaging
University of Pittsburgh
Bsts 225 3550 terrace st
Pittsburgh PA 15261
[hidden email]<mailto:[hidden email]<mailto:[hidden email]%3cmailto:[hidden email]>>
Www.cbi.pitt.edu<http://Www.cbi.pitt.edu><http://www.cbi.pitt.edu/<http://www.cbi.pitt.edu>>
phone:[phone]


Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

[Sripad Ram-2]

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Hi Simon,
Are you referring to the qptiff images or the im3 files? QPTiFF is a newer
file format that can be ported/read relatively easily. If the data was
generated on Vectra 3 then more than likely you have im3 files which store
the MSI data. I have had good success in reading the raw images from im3
files using the bioformat plugin in Matlab (at least I used to many years
ago).  However, I have not been successful in reading the metadata from im3
files.

The IM3 files only store the raw MSI data not the spectrally unmixed
component images. So if you want to do unmixing then you'd have to
implement that yourself. The unmixing algorithm is not difficult to
implement but you will need metadata such as the wavelength bands, step
size of the LCTF, acquisition settings, etc., which is all locked in the
im3 file.

Thanks.

Sripad


On Fri, Jan 22, 2021 at 4:57 AM Watkins, Simon C <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Colleagues, has anyone developed or have a solution for porting data sets
> from the Akoya platform (specifically the Vectra in our case) to an OME
> TIFF?
> We have been given the option or rescanning a ton of slides on one of our
> systems or finding a way to convert previously scanned data
> Thanks for the wisdom and of course stay safe!
> S
>
> Simon C. Watkins Ph.D
> Distinguished Professor and Vice Chair Cell Biology
> Professor Immunology
> Director Center for Biologic Imaging
> University of Pittsburgh
> Bsts 225 3550 terrace st
> Pittsburgh PA 15261
> [hidden email]<mailto:[hidden email]>
> Www.cbi.pitt.edu<http://www.cbi.pitt.edu/>
> phone:[phone]
>

[Mike Nelson]

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*****

Hi Simon,

Just to add a quick note on to what Ajay mentioned about QuPath:
"If the channels in your qptiff have cross talks and plenty of auto
fluorescence then it might be better to unmix them in to component data
using inForm first. You can merge component images using something like
QuPath. On a side note: QuPath works very well with qptiff files, it uses
bio-formats to read qptiff files. It should also be possible to write a
script in QuPath to batch convert files."
The most exciting part for local labs has been that you can stitch together
multiple fields of view (*unmixed tif files* exported from InForm) into
pyramidal whole slide images.
Specific script by Pete Bankhead can be found here:
https://gist.github.com/petebankhead/b5a86caa333de1fdcff6bdee72a20abe

I second checking and or posting on the image.sc forum - I am a big fan :)

And, in relation to Sripad's comment, do you no longer have access to
InForm?

Cheers,
Mike


On Fri, Jan 22, 2021 at 7:45 AM Zalavadia, Ajaykumar <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Simon,
>
> Bio-Formats Command Line Tools supports converting qptiff to ome.tiff,
> bio-fromats seems to carryover metadata (channel names and spatial
> resolution) nicely.
>
> A simple command like this should work:
> bfconvert input.qptiff output.ome.tiff
>
> There other flags you can pass while converting depending on your
> requirements, such as:
> -noflat -bigtiff -tilex 512 -tiley 512 -compression LZW
> -pyramid-resolutions 4 -pyramid-scale 2
>
> If the channels in your qptiff have cross talks and plenty of auto
> fluorescence then it might be better to unmix them in to component data
> using inForm first. You can merge component images using something like
> QuPath. On a side note: QuPath works very well with qptiff files, it uses
> bio-formats to read qptiff files. It should also be possible to write a
> script in QuPath to batch convert files.
>
> I have found Image.sc<https://forum.image.sc/search?q=bfconvert> forums
> to be very resourceful for discussions related to ome.tiff  conversion and
> QuPath<https://qupath.github.io/>.
>
> Best,
> Ajay Zalavadia, Ph.D.
> Imaging Specialist, Imaging Core  |  Lerner Research Institute
> 9500 Euclid Avenue NB10  |  Cleveland, OH 44195
> Phone: [phone] | email: [hidden email]<mailto:[hidden email]>
>
>
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Watkins, Simon C
> Sent: Friday, January 22, 2021 7:57 AM
> To: [hidden email]
> Subject: [EXT] akoya file format
>
> CAUTION CYBER RISK: This email originated from outside of the
> organization. Do not click links or open attachments unless you recognize
> the sender, expected to receive this content and that you believe it to be
> safe. If you feel this email cannot be trusted, please delete the message;
> or submit for investigation with the Report Phishing button or by
> forwarding the email to [hidden email]<mailto:
> [hidden email]>.
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> Post images on http://www.imgur.com<http://www.imgur.com> and include the
> link in your posting.
> *****
>
> Colleagues, has anyone developed or have a solution for porting data sets
> from the Akoya platform (specifically the Vectra in our case) to an OME
> TIFF?
> We have been given the option or rescanning a ton of slides on one of our
> systems or finding a way to convert previously scanned data
> Thanks for the wisdom and of course stay safe!
> S
>
> Simon C. Watkins Ph.D
> Distinguished Professor and Vice Chair Cell Biology
> Professor Immunology
> Director Center for Biologic Imaging
> University of Pittsburgh
> Bsts 225 3550 terrace st
> Pittsburgh PA 15261
> [hidden email]<mailto:[hidden email]<mailto:
> [hidden email]%3cmailto:[hidden email]>>
> Www.cbi.pitt.edu<http://Www.cbi.pitt.edu><http://www.cbi.pitt.edu/<
> http://www.cbi.pitt.edu>>
> phone:[phone]
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
> hard copy. Thank you.
>